Multiple Alignments

[lutfia95]

Dear Authors,

thank you very much for providing the pipeline! I would like to run the pipeline on different genomes together to compute whole genome alignment of different species to use them afterwards in TOGA.
Assume we have 4 assemblies: hg38, mm10, xs1 and ml2. Can I apply something like this:

./make_chains.py hg38 mm10 xs1 ml2 /path/to/hg38.fasta /path/to/mm10.fasta /path/to/xs1.fasta /path/to/ml2.fasta

Best,
Ahmad

[MichaelHiller]

no, the pipeline is strictly pairwise.
For every run, you must specify 1 reference and 1 query genome.